NAME

       samtools merge - merges multiple sorted input files into a single output.

SYNOPSIS

       merge  samtools  merge [-nur1f] [-h inh.sam] [-t tag] [-R reg] [-b list] out.bam in1.bam [in2.bam in3.bam
       ... inN.bam]

DESCRIPTION

       Merge multiple sorted alignment files, producing a single sorted output file that contains all the  input
       records and maintains the existing sort order.

       If  -h  is  specified  the @SQ headers of input files will be merged into the specified header, otherwise
       they will be merged into a composite header created from the input headers.  If in the process of merging
       @SQ  lines  for  coordinate sorted input files, a conflict arises as to the order (for example input1.bam
       has @SQ for a,b,c and input2.bam has b,a,c) then the resulting output file will need to be re-sorted back
       into coordinate order.

       Unless the -c or -p flags are specified then when merging @RG and @PG records into the output header then
       any IDs found to be duplicates of existing IDs in the output header will have a suffix appended  to  them
       to  differentiate  them from similar header records from other files and the read records will be updated
       to reflect this.

       The ordering of the records in the input files must match  the  usage  of  the  -n  and  -t  command-line
       options.   If  they  do  not,  the output order will be undefined.  See sort for information about record
       ordering.

       -1      Use Deflate compression level 1 to compress the output.

       -b FILE List of input BAM files, one file per line.

       -f      Force to overwrite the output file if present.

       -h FILE Use the lines of FILE as `@' headers to be copied to out.bam, replacing  any  header  lines  that
               would  otherwise  be  copied from in1.bam.  (FILE is actually in SAM format, though any alignment
               records it may contain are ignored.)

       -n      The input alignments are sorted by read names rather than by chromosomal coordinates

       -t TAG  The input alignments have been sorted by the value of TAG, then by either position or name (if -n
               is given).

       -R STR  Merge files in the specified region indicated by STR [null]

       -r      Attach an RG tag to each alignment. The tag value is inferred from file names.

       -u      Uncompressed BAM output

       -c      When several input files contain @RG headers with the same ID, emit only one of them (namely, the
               header line from the first file we find that ID in) to the merged output file.   Combining  these
               similar  headers is usually the right thing to do when the files being merged originated from the
               same file.

               Without -c, all @RG headers appear in the output file, with random suffixes added  to  their  IDs
               where necessary to differentiate them.

       -p      Similarly,  for  each  @PG ID in the set of files to merge, use the @PG line of the first file we
               find that ID in rather than adding a suffix to differentiate similar IDs.

       -X      If this option is set, it will allows user to specify customized index file  location(s)  if  the
               data folder does not contain any index file. See EXAMPLES section for sample of useage.

       --no-PG Do not add a @PG line to the header of the output file.

EXAMPLES

       o Attach the RG tag while merging sorted alignments:

           perl -e 'print "@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt
           samtools merge -rh rg.txt merged.bam ga.bam 454.bam

         The  value  in a RG tag is determined by the file name the read is coming from. In this example, in the
         merged.bam, reads from ga.bam will be attached RG:Z:ga, while  reads  from  454.bam  will  be  attached
         RG:Z:454.

       o Include customized index file as a part of arugments:

           samtools merge [options] -X <out.bam> </data_folder/in1.bam> [</data_folder/in2.bam> ... </data_folder/inN.bam>] </index_folder/index1.bai> [</index_folder/index2.bai> ... </index_folder/indexN.bai>]

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-sort(1), sam(5)

       Samtools website: <http://www.htslib.org/>